Originally Posted by
MikeFromTokyo
If you want to stick to the $300~/night range, IMO some of the best values would be the Hyatt Regency, Hilton, and Century Southern Tower. These hotels are in the Shinjuku area, where there are a great many department stores, including Takashimaya Times Square, Isetan, Odakyu, etc...
If you can increase the budget a bit, then the very best located hotel would be the Mandarin Oriental. It is right next to Takashimaya and Mitsukoshi in Nihombashi, and very close to Ginza as well. Even a standard room is spacious at 50 square meters, and will have impressive views. Booking through Amex FHR will get you breakfast, an upgrade, and other benefits at MO or any of the other FHR hotels in Tokyo.
You might also consider the Grand Hyatt in Roppongi Hills. Roppongi is also good for shopping, and it is easy to get around the city by subway.
After much research, we are going with the Peninsula. The rates for top hotels in Tokyo are much less than the rates in New York and even Hong Kong. Do you have advise for the best way to get to the hotel from NRT? The hotel car service is MUCH more expensive than in HKG. Thinking either limo bus or train, how difficult are these options and are there any other options I don't know about?